Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101148
Name   oriT_pSM90_Rh15 in_silico
Organism   Rhizobium ruizarguesonis strain SM90
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIMP01000006 (95170..95211 [-], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      22..27, 31..36  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 42 nt

>oriT_pSM90_Rh15
GGCTCCAAGGGCGCAATTATACGTCGCGATGCGACGCGTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1145 GenBank   WP_130821156
Name   traA_ELH38_RS33810_pSM90_Rh15 insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123229.60 Da        Isoelectric Point: 9.7679

>WP_130821156.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPAGAPSWVRSLTADR
SVAGASEAFWNKVEAFEKRADAQLARDLTIALPLELSAEQNIALVRDFVEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLSEDGFGSKKVPVIGDDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRVDGRSYEKQGIELEPTIHLGEGAKAIERKAEQQGVRPELERIELNEQRRSENARRILKNPLIVLDL
ITREKSVFDERDVAKVVHRYIDDPAVFQQLMIRIILNPDVLRLQRDSVDFATGNKQPARYSTRAMIRLEA
TMARQARWLSAKETQAVSEAVLGATFLRHERLSDEQKAAIERITGPHRIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIESRTLASWELRWNRGRDVLDDKTIFVMDEAGMVASKQMAGFVD
TVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALSAYG
ANVKITGERLKAEAVERLIAAWNQDYDQSKTTLILAHLRRDVRVLNVMAREKLVERGVVGEGKIFKTADG
ERRFDAGDQIVFLKNEGSLGLKNGMIGHVVEAQPNRIVAVAGEGDYRRQVIVEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGTRSFSFNGGLAKVLSRKNAKETTLDYERGQLY
REALRFAENRGLHIVQVARTLVRDQLDWTLRQKARLVDLGQRLAAFAARLGLAQSLNIQTMKEAAPMVEG
IKTFSGSAADTVGDKLGADPTLKRQWEEVSARFSYVFADPETAFRAMNFDVVLVDKQAAKLILQKLEGEP
ASIGPLRGKTGILATKSERESRRVAEVNVPALKRDLEQYLRMRETATMRHQADEQALRQRVSIEIPALSP
AAHVVLERVRDAIDRNDLPAAMAYALSNRETKLEIDGFNRAVTERFGERTLLSNAAQEPSGTLYEKLSEG
MKPEQKEQLKQAWPVMRTAQQLGAHERTIQSLRQAEEQRLTQRQAPVLKQ

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(855-951)

AAA domain (AAA_30)

(382-566)


  Protein structure



No available structure.




T4CP

ID   712 GenBank   WP_130821130
Name   t4cp2_ELH38_RS33660_pSM90_Rh15 insolico UniProt ID   _
Length   826 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 826 a.a.        Molecular weight: 92474.43 Da        Isoelectric Point: 5.9517

>WP_130821130.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALKPFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAVRVATEDYPTDQASHFPDPVTRAIDAERRSHFQKERGHYESRHALILTWRPPEPRRSGLTR
YVYSDIGSRSATYADKALETFLTSIREVEQYIANVVSIRRMTTRETSERGGYRMARYDELFQFIRFCITG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNTLDRMPLTYRWSSRFVF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVI
FDEDHHRLQENCEAIRRLVQAEGFGARIETLNATDAFIGSLPGVSYANIREPLINTRNLADLIPLNSIWS
GSPVAPCPFYPPASPPLMQVATGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYAEAQVFA
FDKGGSMLPLTLGLAGNHYNIGGEQPDRAEEGRAGEARGLSFCPLAELAADGDLAWASEWIEMLVALQGV
TVTPDYRNAISRQLALMAKSRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFE
IEELMNMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPAFRDKIREWLKVLRKANCAVVLAT
QSISDAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKRDYYVVSPEGRR
LFDMALGPVALSFVGASGKEDLKRIRALHLEHGANWPLHWLQQRGIAHAETLLPIE

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(186-400)

  Protein structure



No available structure.



ID   713 GenBank   WP_130821159
Name   traG_ELH38_RS33825_pSM90_Rh15 insolico UniProt ID   _
Length   636 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 636 a.a.        Molecular weight: 68350.39 Da        Isoelectric Point: 9.4956

>WP_130821159.1 Ti-type conjugative transfer system protein TraG [Rhizobium ruizarguesonis]
MTANRLLLAILPAAIMIAAMVITSGMEHRLAALGTNAQAKLMLGRAGLALPYVVVAAIGGMALSAANGSA
NIKAVGLSVIVGNGMAIAVAILRETIRLTGFAANIPAEQSVLTYIDPATMLGTIAAFVSGVFALRVALRG
NAAFATASPKRIGGRRAVHGGADWMKLPDAAKLFPEHGGIVIGERYRVDRDSVAAMPFRADEAQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVSEHRRQAGRKVIVLD
PTATDVGFNALDWIGRHGNTKEEDIVAVATWIMTDNARMASARDDFFRASAMQLLTALIADVCLSGHTDA
KDQTLRRVRANLSEPEPQLRARLTKIYEGSASDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGNSFSTDDLADGETDIFIALDLKVLEAHPGLARVVIGSFLNAIYNRNGDVKGRTLFLLDEVARLGY
LRILETARDAGRKYAITLAMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSKQLSRRPLILPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMKACVG
DNRFQR

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(163-633)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 56876..66563

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH38_RS33625 (ELH38_33650) 52192..53436 - 1245 WP_130821123 plasmid replication protein RepC -
ELH38_RS33630 (ELH38_33655) 53593..54588 - 996 WP_130821124 plasmid partitioning protein RepB -
ELH38_RS33635 (ELH38_33660) 54673..55863 - 1191 WP_130821125 plasmid partitioning protein RepA -
ELH38_RS33640 (ELH38_33665) 56241..56879 + 639 WP_130821126 acyl-homoserine-lactone synthase TraI -
ELH38_RS33645 (ELH38_33670) 56876..57847 + 972 WP_130821127 P-type conjugative transfer ATPase TrbB virB11
ELH38_RS33650 (ELH38_33675) 57837..58241 + 405 WP_130821128 conjugal transfer pilin TrbC virB2
ELH38_RS33655 (ELH38_33680) 58234..58533 + 300 WP_130821129 conjugal transfer protein TrbD virB3
ELH38_RS33660 (ELH38_33685) 58545..61025 + 2481 WP_130821130 conjugal transfer protein TrbE virb4
ELH38_RS33665 (ELH38_33690) 60997..61806 + 810 WP_130821131 P-type conjugative transfer protein TrbJ virB5
ELH38_RS33670 (ELH38_33695) 61803..62030 + 228 WP_130821132 entry exclusion protein TrbK -
ELH38_RS33675 (ELH38_33700) 62024..63214 + 1191 WP_130821133 P-type conjugative transfer protein TrbL virB6
ELH38_RS33680 (ELH38_33705) 63232..63894 + 663 WP_130821134 conjugal transfer protein TrbF virB8
ELH38_RS33685 (ELH38_33710) 63912..64763 + 852 WP_130821194 P-type conjugative transfer protein TrbG virB9
ELH38_RS33690 (ELH38_33715) 64763..65239 + 477 WP_130821135 conjugal transfer protein TrbH -
ELH38_RS33695 (ELH38_33720) 65247..66563 + 1317 WP_130821136 IncP-type conjugal transfer protein TrbI virB10
ELH38_RS33700 (ELH38_33725) 66711..67487 - 777 WP_130821137 SDR family NAD(P)-dependent oxidoreductase -
ELH38_RS33705 (ELH38_33730) 67529..68707 - 1179 WP_245502936 LacI family DNA-binding transcriptional regulator -
ELH38_RS33710 (ELH38_33735) 68822..69886 - 1065 WP_130821138 aldo/keto reductase -

Host bacterium

ID   1592 GenBank   NZ_SIMP01000006
Plasmid name   pSM90_Rh15 Incompatibility group   -
Plasmid size   130694 bp Coordinate of oriT [Strand]   95170..95211 [-]
Host baterium   Rhizobium ruizarguesonis strain SM90

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -